create_se: Create a SummarizedExperiment given some metadata

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Create a SummarizedExperiment given some metadata

Description

This function was taken from create_expt() and repurposed to create SummarizedExperiments.

Usage

create_se(
  metadata = NULL,
  gene_info = NULL,
  count_dataframe = NULL,
  sanitize_rownames = FALSE,
  sample_colors = NULL,
  title = NULL,
  notes = NULL,
  countdir = NULL,
  include_type = "all",
  include_gff = NULL,
  file_column = "file",
  id_column = NULL,
  savefile = NULL,
  low_files = FALSE,
  annotation = "org.Hs.eg.db",
  palette = "Dark2",
  round = FALSE,
  tx_gene_map = NULL,
  ...
)

Arguments

metadata	Filename or table of metadata about the samples of interest.
gene_info	Annotations for the genes in the count data.
count_dataframe	Optional table of counts.
sanitize_rownames	Clean up unruly gene IDs?
sample_colors	Specify the colors for the samples?
title	Provide a title for the experiment.
notes	Provide arbitrary notes.
countdir	(deprecated) Directory containing count tables.
include_type	Used to specify types of genes/annotations to use.
include_gff	Keep a copy of the gff with the data?
file_column	Metadata column containing the counts for each sample.
id_column	Non-default column containing the sample IDs.
savefile	Filename to which to save a rda file of the data structure.
low_files	I don't remember this, I bet it is deprecated.
annotation	orgDB associated with this, primarily used with gsva-like tools.
palette	Color palette when auto-choosing colors for the samples.
round	Round the data if/when it is not integer?
tx_gene_map	When using tximport, use this to convert from transcripts to genes.
...	Extra options.

See Also

[summarizedExperiment]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.